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Human Teneurin-4 C-rich domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other From unpublished anomalous experiment
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.5 293 0.085 M HEPES pH 7.5,
1.7 v/v % PEG-400,
1.7 M (NH4)2SO4,
15 w/v % glycerol
Crystal Properties Matthews coefficient Solvent content 2.34 47.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.343 α = 90 b = 66.343 β = 90 c = 66.343 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2021-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.7749 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.4 46.91 100 0.184 0.186 0.029 0.999 14 41.2 19462
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 100 13.184 2.082 0.718 39.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT From unpublished anomalous experiment 1.4 33.19 18241 927 98.69 0.1556 0.1548 0.155 0.1705 0.1715 RANDOM 23.684
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.117 r_dihedral_angle_3_deg 13.723 r_dihedral_angle_1_deg 6.966 r_rigid_bond_restr 2.648 r_angle_refined_deg 1.703 r_angle_other_deg 1.555 r_chiral_restr 0.109 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.117 r_dihedral_angle_3_deg 13.723 r_dihedral_angle_1_deg 6.966 r_rigid_bond_restr 2.648 r_angle_refined_deg 1.703 r_angle_other_deg 1.555 r_chiral_restr 0.109 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 598 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction